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Fu S, Ding M, Liang Q, Yang Y, Chen M, Wei X, Wang A, Liao S, Ye J. The key differentially expressed genes and proteins related to immune response in the spleen of pufferfish (Takifugu obscurus) infected by Aeromonas hydrophila. FISH & SHELLFISH IMMUNOLOGY 2019; 91:1-11. [PMID: 31085326 DOI: 10.1016/j.fsi.2019.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
The immune mechanism elicited in pufferfish (Takifugu obscurus) against the invasion of Aeromonas hydrophila is still poorly understood. We examined the spleen of pufferfish at the transcriptome and proteome levels by using Illumina-seq and TMT coupled mass spectrometry after 12 h infection by A. hydrophila, respectively. A total of 2,339 genes (1,512 up-regulated and 827 down-regulated) and 537 (237 up-regulated and 300 down-regulated) proteins were identified. GO and KEGG analyses revealed that the responses to stimulus were the main biological processes, intestinal immune network for IgT production and calcium signaling pathway. Fourteen genes (8 up-regulated and 6 down-regulated) and proteins (5 up-regulated and 9 down-regulated) involved immune responses or signal transduction were validated by qRT-PCR and parallel reaction monitoring to confirm the reliability of the transcriptomic and proteomic analyses, respectively. Moreover, qRT-PCR and flow cytometry were used to detect dynamics of the genes in calcium signaling pathway and changes of concentration of cytoplasm Ca2+ in spleen cells within a 72 h challenge. This study provides the findings regarding immune response, especially intestinal immune network for IgT production pathway and calcium signaling pathway at the molecular, protein and cellular in pufferfish after infection by A. hydrophila. These results would provide a new insight and molecular targets into the response to pathogenic infection in pufferfish.
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Affiliation(s)
- Shengli Fu
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Mingmei Ding
- School of Medicine, Sun Yat-Sen University, Guangzhou, 510006, PR China
| | - Qingjian Liang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Yanjian Yang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Meng Chen
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Xiufang Wei
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Anli Wang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Shaoan Liao
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China.
| | - Jianmin Ye
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China.
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Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis. Sci Rep 2019; 9:8504. [PMID: 31186469 PMCID: PMC6560038 DOI: 10.1038/s41598-019-44870-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/20/2019] [Indexed: 11/08/2022] Open
Abstract
Macaca fascicularis, also known as the cynomolgus macaque, is an important non-human primate animal model used in biomedical research. It is an Old-World primate widely distributed in Southeast Asia and is one of the most abundant macaque species in Malaysia. However, the genetic structure of wild cynomolgus macaque populations in Malaysia has not been thoroughly elucidated. In this study, we developed genic-simple sequence repeat (genic-SSR) markers from an in-house transcriptome dataset generated from the Malaysian cynomolgus macaque via RNA sequencing, and applied these markers on 26 cynomolgus macaque individuals. A collection of 14,751 genic-SSRs were identified, where 13,709 were perfect SSRs. Dinucleotide repeats were the most common repeat motifs with a frequency of 65.05%, followed by trinucleotide repeats (20.55%). Subsequently, we designed 300 pairs of primers based on perfect di- and trinucleotide SSRs, in which 105 SSRs were associated with functional genes. A subset of 30 SSR markers were randomly selected and validated, yielding 19 polymorphic markers with an average polymorphism information content value of 0.431. The development of genic-SSR markers in this study is indeed timely to provide useful markers for functional and population genetic studies of the cynomolgus macaque and other related non-human primate species.
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Zhang Z, Du H, Yang C, Li Q, Qiu M, Song X, Yu C, Jiang X, Liu L, Hu C, Xia B, Xiong X, Yang L, Peng H, Jiang X. Comparative transcriptome analysis reveals regulators mediating breast muscle growth and development in three chicken breeds. Anim Biotechnol 2019; 30:233-241. [PMID: 30601081 DOI: 10.1080/10495398.2018.1476377] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Objective: The goal of this study was to investigate the mechanisms of muscle growth and development of three chicken breeds. Participants: Eighteen chickens, including three different breeds with different growth speeds (White Broiler, Daheng, and Commercial Layers of Roman), were used. Methods: Total RNA from breast muscle of these chickens was subjected to a gene expression microarray. Differentially expressed genes (DEGs) were screened and functional enrichment analysis was performed using DAVID. Seven DEGs were confirmed by quantitative reverse transcription PCR. Results: Overall, 8,398 DEGs were found among the different lines. The DEGs between each two lines that were unique for a developmental stage were greater than those that were common during all stages. Functional analysis revealed that DEGs across the entire developmental process were primarily involved in positive cell proliferation, growth, cell differentiation, and developmental processes. Genes involved in muscle regulation, muscle construction, and muscle cell differentiation were upregulated in the faster-growing breed compared to the slower-growing breed. DEGs including myosin heavy chain 15 (MYH15), myozenin 2 (MYOZ2), myosin-binding protein C (MYBPC3), insulin-like growth factor 2 (IGF2), apoptosis regulator (BCL-2), AP-1 transcription factor subunit (JUN), and AP-1 transcription factor subunit (FOS) directly regulated muscle growth or were in the center of the protein-protein interaction network. Pathways, including the extracellular matrix (ECM)-receptor interaction, mitogen-activated protein kinase (MAPK) signaling pathway, and focal adhesion, were the most enriched DEGs between lines or within lines under different developmental stages. Conclusions: Genes involved in muscle construction and cell differentiation were differentially expressed among the three breeds.
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Affiliation(s)
- Zengrong Zhang
- a Sichuan Animal Science Academy , Chengdu , Sichuan , China.,b Sichuan Daheng Poultry Breeding Company , Chengdu , Sichuan , China
| | - Huarui Du
- a Sichuan Animal Science Academy , Chengdu , Sichuan , China
| | - Chaowu Yang
- a Sichuan Animal Science Academy , Chengdu , Sichuan , China
| | - Qingyun Li
- c Animal Breeding and Genetics Key Laboratory of Sichuan Province , Chengdu , Sichuan , China
| | - Mohan Qiu
- a Sichuan Animal Science Academy , Chengdu , Sichuan , China
| | - Xiaoyan Song
- b Sichuan Daheng Poultry Breeding Company , Chengdu , Sichuan , China
| | - Chunlin Yu
- c Animal Breeding and Genetics Key Laboratory of Sichuan Province , Chengdu , Sichuan , China
| | - Xiaoyu Jiang
- c Animal Breeding and Genetics Key Laboratory of Sichuan Province , Chengdu , Sichuan , China
| | - Lan Liu
- c Animal Breeding and Genetics Key Laboratory of Sichuan Province , Chengdu , Sichuan , China
| | - Chenming Hu
- c Animal Breeding and Genetics Key Laboratory of Sichuan Province , Chengdu , Sichuan , China
| | - Bo Xia
- a Sichuan Animal Science Academy , Chengdu , Sichuan , China
| | - Xia Xiong
- a Sichuan Animal Science Academy , Chengdu , Sichuan , China
| | - Li Yang
- c Animal Breeding and Genetics Key Laboratory of Sichuan Province , Chengdu , Sichuan , China
| | - Han Peng
- b Sichuan Daheng Poultry Breeding Company , Chengdu , Sichuan , China
| | - Xiaosong Jiang
- a Sichuan Animal Science Academy , Chengdu , Sichuan , China.,b Sichuan Daheng Poultry Breeding Company , Chengdu , Sichuan , China
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Ee Uli J, Yong CSY, Yeap SK, Alitheen NB, Rovie-Ryan JJ, Mat Isa N, Tan SG. RNA sequencing of kidney and liver transcriptome obtained from wild cynomolgus macaque (Macaca fascicularis) originating from Peninsular Malaysia. BMC Res Notes 2018; 11:923. [PMID: 30577850 PMCID: PMC6303865 DOI: 10.1186/s13104-018-4014-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/12/2018] [Indexed: 01/22/2023] Open
Abstract
Objective Using high-throughput RNA sequencing technology, this study aimed to sequence the transcriptome of kidney and liver tissues harvested from Peninsular Malaysia cynomolgus macaque (Macaca fascicularis). M. fascicularis are significant nonhuman primate models in the biomedical field, owing to the macaque’s biological similarities with humans. The additional transcriptomic dataset will supplement the previously described Peninsular Malaysia M. fascicularis transcriptomes obtained in a past endeavour. Results A total of 75,350,240 sequence reads were obtained via Hi-seq 2500 sequencing technology. A total of 5473 significant differentially expressed genes were called. Gene ontology functional categorisation showed that cellular process, catalytic activity, and cell part categories had the highest number of expressed genes, while the metabolic pathways category possessed the highest number of expressed genes in the KEGG pathway analysis. The additional sequence dataset will further enrich existing M. fascicularis transcriptome assemblies, and provide a dataset for further downstream studies. Electronic supplementary material The online version of this article (10.1186/s13104-018-4014-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joey Ee Uli
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Christina Seok-Yien Yong
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University, Sepang, Selangor, Malaysia
| | - Noorjahan Banu Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Jeffrine J Rovie-Ryan
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, Kuala Lumpur, Malaysia
| | - Nurulfiza Mat Isa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Soon Guan Tan
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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